A protester opposing Egyptian President Mohamed Morsi gestures at riot police during clashes as a fire (rear) is seen at the French Lycee School along Mohamed Mahmoud street, which leads to the Interior Ministry, near Tahrir Square in Cairo, last month. This is the cover story in the Feb. 11 issue of The Christian Science Monitor Weekly.

Mohsen al-Domiati, a cap pulled low over his forehead, stands dejectedly near a mosque in the Egyptian city of Port Said, which recently has been a source of seething protests against the rule of President Mohamed Morsi. He stares off into space vacantly. His eyes are red.

Just hours earlier, Mr. Domiati attended the funeral of his brother, Mohamed, who was killed the day before by police cracking down on the protesters. According to Domiati, his brother was an innocent victim: Mohamed, a waiter at a local restaurant who has an 18-month-old daughter, was heading out to get groceries just after sunset. Amid the chaos in the streets, police started shooting. A guy next to Mohamed fell down. He tried to save him. Moments later, he was shot in the head.

Now Domiati, who says his brother died in the simple quest to get some yogurt, has become a committed opponent of the president. Already dubious of the heavy-handed rule of Mr. Morsi, he vows to defy the new regime any way he can.

"As long as there is no justice, we are not going to stop protesting," he says. "This is going to end only when they give us [our] rights. We are eventually going to die, but we are not going alone. We're going to take lots of them with us."

Domiati's words are a harsh reminder to Morsi of one of the truisms of history, particularly in the modern Middle East: Taking power is one thing. Governing is something far different.

Just seven months ago, the president and the Muslim Brotherhood, the 80-year-old Egyptian Islamist movement that has inspired imitators from Morocco to the southern Philippines, seemed to be at the pinnacle of power. Morsi had just been sworn in as leader of the Arab world's largest state, becoming arguably the most powerful Islamist politician in history.

In the 17 months since Egypt's longstanding dictator Hosni Mubarak was toppled by a popular uprising, the Brothers had marched from one electoral victory to the next. Many people wondered if an era of Islamist political dominance had arrived in the region to replace the secular dictatorships that marked much of the 20th century.

Today, all that euphoria seems almost a quaint memory. Months of resistance to Morsi's rule culminated in late January with furious protesters and angry mobs doing battle with government forces across much of the country: in Cairo's iconic Tahrir Square; at a nearby luxury hotel; and in the gritty port cities of Suez, Ismailiya, and Port Said along the Suez Canal, Egypt's economic lifeline.

In the canal zone, Morsi was forced to declare a state of emergency, and called the military out into the streets, granting them the sort of arrest and prosecution powers that Mr. Mubarak's state not long ago was using to control the Brothers. The violence has had an anarchic edge, fueled by defiance against a state that Morsi now symbolizes but without any core political message beyond calls for justice for the martyrs.

"Mubarak with a beard," says Mohamed al-Mesri, a young protester in Cairo, of Morsi.

All this has no doubt shaken Morsi's confidence and that of anyone around him who expected the Brotherhood to ease comfortably into power and set about the business of achieving its long-held dream: to mold Egypt into a state that looks to the Quran rather than modern history in crafting its laws and institutions.

The seething distrust in the streets – for the Muslim Brotherhood, for the state security institutions that Egypt's new leaders have cozied up to so successfully – is not unique to Egypt in the region, nor are its enormous economic and educational challenges. In Syria, the civil war has left the country in tatters, and if the rebels there win, a swift Sunni Islamist consolidation looks even less likely than in Egypt.

What happens in Egypt will provide a road map and inspiration – or a warning – to other Islamist groups from Syria, where the bloody civil war involves a number of Islamist militias, to Lebanon to Libya. In small Tunisia, the Islamist Al Nahda party, the Brotherhood's more pragmatic kin, also holds power.

(While Turkey has had Islamist-led, freely elected governments for years, the country, as a non-Arab state, is different culturally and historically, making it an unlikely model for its neighbors.)

Across the Arab world, Islamist political movements are on the move after decades of state repression and marginalization, raising questions in some circles of whether the events of 1979 in Iran, when the shah was replaced by Ayatollah Ruhollah Khomeini, are being replicated 30 years later with a Sunni twist.

The biggest prize will remain Egypt, the wellspring of modern Islamist political movements, and the linchpin in the cold peace that has endured since the Camp David accords were signed in 1978.

The discontent within Egypt and the reality that Morsi won the presidency with only 51 percent of the vote against 49 percent for Ahmed Shafiq, a former prime minister under Mubarak, shows that what can at times seem an inexorable Sunni Islamist rise in the region is actually hotly contested and controversial.

Will the Brothers lead Egypt a decade from now? Will their ideological allies do likewise in Libya, Tunisia, or in Syria? That is far from guaranteed.

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In US policymaking circles, all this is being greeted with shudders and confusion about whether durable regional democracies can rise under the leadership of groups like the Brotherhood, whether longstanding security arrangements will be upended, whether even a new era of confrontation between Arab states and the West looms.

But the precise nature of those stakes is often misunderstood. Take the comparisons to the Islamic revolution in Iran. Then, an entire national order was upended with the ouster of the shah, as Mr. Khomeini and his allies carried out a bloody purge of leftists and other nationalists who had participated in the revolution. Fueled by anti-British and anti-American slogans and intent, revolution leaders installed a political order with a senior Shiite cleric as "supreme leader" that persists to this day.

In Egypt and Tunisia something very different has been under way, which Olivier Roy, a leading historian of Islamist movements, calls a "conservative and paradoxically pro-western 'counter-revolution.' "

In an article in the British magazine New Statesman in December, he wrote: "Consider Egypt. If the president, Mohamed Morsi, is denounced in Tahrir Square as the new Mubarak (and not the new Khomeini), it is because his opponents have grasped that his aim is to establish an authoritarian regime using classical means (appealing to the army and controlling the apparatus of the state)."

"There is a very strong sense of disorientation about how to build a relationship with the new Egypt," says Steven Cook, the Hasib J. Sabbagh senior fellow for Middle Eastern Studies at the Council on Foreign Relations in Washington. "In Washington at one level there is recognition that there's a huge change, and at another level we're still going about business as usual."

* * *

The record of the Muslim Brotherhood so far on its commitment to a full and open democracy is decidedly mixed. It rushed through a new Egyptian Constitution that allows for military trials of civilians, strict restrictions on free speech, and a role for the Muslim scholars at Al Azhar in Cairo to decide whether legislation complies with sharia, or Islamic law.

Government prosecutors have eagerly taken up a spate of legal complaints against journalists and opposition figures for "insulting" either Islam or Morsi himself.

The new president has also allied himself closely with the politically powerful military. The Brothers wrote a constitution for the country that in the first sentence credits the armed forces with supporting the uprising against Mubarak, which isn't really true.

They've protected the military's budget and sprawling business empire from civilian scrutiny, and preserved the military's right to try civilians in its own courts, which have been used extensively to silence political dissent. In exchange, they've received the backing of senior generals, but lost the respect of millions of Egyptians, particularly among the young who were the engine of the uprising in 2011.

"He's looking after his party's interests, not our interests," says Mustafa al-Eid, an Internet entrepreneur who joined protests against the military in 2011 and 2012 but has walked away from politics, disgusted that Egypt's new leaders seem as disengaged with the problems of common citizens as their predecessors.

The Brothers have insisted that they're the democrats – they won the presidency fair and square, after all – and that their opponents want to impose their will on the majority.

Mahmoud Hussein, secretary-general of the Muslim Brotherhood, told government-owned Arham Online in late January that "the opposition made a serious mistake when it resorted to lying and disinformation and when it used undemocratic methods to change things." He attacked the National Salvation Front (NSF), a loose coalition of secular-leaning politicians, for its complaints about Egypt's new Constitution, which was approved in a national referendum.

"This is a punishable offense," he said of the NSF's calls to rewrite the document. "To say that you want to bring down a constitution that was approved by the people – this is a remark that befits a thug, not a politician."

Mr. Hussein's comments are fairly typical of the recent tone from the Brothers, who have shown little willingness to consider crafting rules that protect against a tyranny of the majority, or an understanding of the risk that can ultimately pose to national cohesion.

"To the extent that you can draw any conclusions about MB [Muslim Brotherhood] now is that they clearly have a majoritarian view of politics," says Mr. Cook. If the Brothers get their way, Egypt "will be an illiberal polity," he says.

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While all this may be bad for Egyptian liberals, it isn't necessarily a problem for US security interests in the region. After all, one of America's closest friends in the Arab world is Saudi Arabia, one of the most repressive countries when it comes to the rights of women and minorities.

This is the state of play seven months into the Muslim Brotherhood's rule of Egypt: The Islamist group that the United States long feared would rise to power if the dictatorship fell has been eager for good relations with the US, repeatedly sending signals to Washington that when it comes to Israel or regional security relationships, what was Mubarak's business is now the Brotherhood's business.

Despite controversy over anti-Semitic remarks made by Morsi in 2010, his government has repeatedly pledged to stand by the Camp David accords signed by Anwar Sadat, who was assassinated by a member of Egypt's Islamic Jihad in 1981.

When all-out war loomed between Hamas, an offshoot of the Brotherhood in the Gaza Strip, and Israel last September, Morsi worked with the US and Israel to bring about a temporary peace, much as Mubarak worked with the US and Israel before him. And he's desperate to receive an International Monetary Fund loan to stabilize the collapsing Egyptian pound and a weak economy. He knows he can't get it without US support.

None of this has been overlooked by Morsi's critics. In the recent rioting, thousands of angry protesters shouted irhal! ("go!") at Morsi, much as they did at Mubarak two years ago in defiance of volleys of tear gas. In some cities, protesters specifically targeted Brotherhood offices, and the Army had to be called out in Alexandria and Suez to protect government buildings.

Torched, too, were the offices of a local Al Jazeera affiliate, which is another stunning reminder of how much has changed in the past two years. During the so-called Arab Spring, Al Jazeera put a face and voice to a revolutionary demand that electrified the whole region, beaming first the Tunisian and then the Egyptian uprisings into practically every living room and coffee shop from Morocco to Syria. The network helped fuel a sense of common Arab identity around calls for an end to torture and state abuse in countries as different as Syria and Bahrain.

But today, Al Jazeera is seen as resolutely pro-Muslim Brotherhood, as is Qatar, the tiny kingdom that funds it. The Brotherhood, a late supporter of the anti-Mubarak uprising, is also viewed by many as molding the old Mubarak playbook to its own needs rather than representing the clean break from the past that many had hoped for in 2011.

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For all their fury, the latest protests are unlikely to achieve the same results as the far larger and more united rebellion that drove out Mubarak. The protesters' calls carry nowhere near as much moral force. Morsi, after all, is the first freely elected president in Egyptian history, and Mubarak was a military-backed dictator who had been in power for 30 years. Morsi has been in office for barely seven months.

While Egypt's various opposition forces have been in disarray – unable to translate street protests into policy achievements or formal power – the Brothers have also been focusing on outreach to the poor. On Jan. 25, as violence swept parts of Egypt, Brotherhood members were focusing on winning the hearts and minds of Egyptians by selling vegetables, food, and clothes for reduced prices, and offering free medical care.

Yousuf Kamal is a member of the Muslim Brotherhood's Ezbet el Nakhl branch, and he helped organize the charity programs. Ezbet el Nakhl is near the end of Cairo's metro line, one of the neighborhoods that sprang up to house Cairo's growing population. It is a simple place, full of four-story brick apartment buildings whose residents brighten the neighborhood by painting their balconies turquoise and peach.

"With these acts, we want to convey a message," says Mr. Kamal. "We have a country to build. We have to work and do some good works to help people. Some people go to millioneyas in the squares," he says, using the word that in Egypt refers to a million-person protest. "But we make a millioneya for good deeds."

Nevertheless, Egypt and the rest of the region are in many ways still waiting for their revolutions, and if and when they come they could sweep away Islamist leaders just as previous uprisings removed secular dictators like Mubarak and Libya's Muammar Qaddafi. And, Ms. Wittes points out, "Islamist" means very different things from group to group, and country to country.

"In Syria, there are people putting forward visions that are putting real anxiety into the US conversation, but in Libya you have Islamists who are losing," she says. "You can't look across the region and say it's all the same thing, that's No. 1. No. 2 is we can't assume, and for the sake of US interests it's unwise to assume, that the rise of Islamist interests now means that they are ascendant and are triumphant and are going to keep on winning."

In Tunisia, for instance, Islamist leaders have sought to reach out to the US and Europe, as has the weak government in Libya, which owes its victory over Mr. Qaddafi to a NATO air campaign that made its revolution possible.

In other parts of the region, the rise of Sunni Islamists has clearly darker overtones, perhaps nowhere more so than in Syria, where the bloody civil war has raged for two years now and claimed more than 50,000 lives. There, the Baathist dictatorship of Bashar al-Assad is holding firm against an uprising that has powerful components from both the local version of the Muslim Brotherhood, and, more worryingly, jihadis whose approach to Islam is more akin to that of Al Qaeda.

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What sort of order will emerge if Mr. Assad falls? The aftermath there will certainly be far messier than the ones in relatively homogenous countries like Egypt and even Libya. Many experts worry the country could experience a repeat of the sectarian bloodletting that swept Iraq after Saddam Hussein's Baathist dictatorship was smashed by the US in 2003.

Then, tens of thousands of refugees poured into Syria and Jordan, as Iraq's Sunni Arab minority struggled against the country's Shiite Arab majority, and lost. Today, Iraq's politics are unstable and violent, and could grow even more so if a Sunni Islamist government comes to power in Syria, a possible ally to the Sunni majority areas in northern Iraq and in Anbar Province, along the Syrian border.

A violent spillover into Lebanon, wrenched by its own civil war in the 1980s, is also possible. Both Iraqi Shiites and Hezbollah have been fighting inside Syria to save Assad, encouraged by Iran, which fears for its own regional standing if its closest ally, Assad, falls.

"A serious breakdown in Syria is going to affect Turkey, Lebanon, with refugees spread across these countries," says Cook. "Iraq has been squeezed by this situation and the Iranians aren't going to give it up too easily."

This all makes for an untidy, dangerous aftermath – but certainly not one of "Islamist" triumph across the region.

What comes next? No one knows for sure.

"The fact that Islamists would do quite well in early open competition in the Arab world should surprise no one," says Wittes. "They had the most grass-roots support, institutions, and since authoritarian states were very good at shutting down secular parties, Islamists had a way of reaching around it, by using mosques. Because they faced no real competition, they could be an empty vessel for everyone's hopes and fears."

That luxury – of being the principled opposition – no longer belongs to the Brothers in Egypt. As Mohamed Moshen, whose brother-in-law was killed in Port Said and who voted for Morsi, puts it: "Hosni Mubarak and Mohamed Morsi are one and the same. I thought he [Morsi] was a respectful person. I thought he knew Islam."